ENST00000558792.6:n.572-4270C>T

Variant names:

• chr15-47778678-G-A
• rs11855291
• ENST00000558792.6:n.572-4270C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558792.6(LINC01491):​n.572-4270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,014 control chromosomes in the GnomAD database, including 5,541 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (5541 hom., cov: 33)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482
• Publications: 0 publications found

Genes affected

LINC01491 (HGNC:51148): (long intergenic non-protein coding RNA 1491)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.572-4270C>T		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.580-4270C>T		intron_variant	Intron 6 of 6
LINC01491	ENST00000653152.1	n.620-4270C>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40339 AN: 151896 Hom.: 5539 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.265 AC: 40355 AN: 152014 Hom.: 5541 Cov.: 33 AF XY: 0.266 AC XY: 19777 AN XY: 74276

African (AFR) AF: 0.240 AC: 9938 AN: 41462

American (AMR) AF: 0.231 AC: 3532 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3464

East Asian (EAS) AF: 0.152 AC: 788 AN: 5180

South Asian (SAS) AF: 0.260 AC: 1251 AN: 4818

European-Finnish (FIN) AF: 0.339 AC: 3579 AN: 10546

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19366 AN: 67960

Other (OTH) AF: 0.266 AC: 561 AN: 2108

Alfa AF: 0.291 Hom.: 2314

Bravo AF: 0.249

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8
DANN	Benign	0.39
PhyloP100		0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11855291; hg19: chr15-48070875;